refactor: implement RoutableSuperKmer and update k-mer indexing pipeline

Replace raw SuperkMer routing with a new RoutableSuperKimer type that embeds canonical sequences and precomputed minimizers, enabling direct partition routing via hash. Update the build pipeline to yield RoutableSuperKmers throughout (builder, scatterer), refactor FASTA/unitig export commands to use the new type and compressed outputs (.fasta.gz, .unitigs.fasta.zst), revise SuperKmer header to store n_kmers instead of seql (avoiding 256-byte wrap), and update documentation to reflect minimizer-based theory, two evidence-encoding strategies for unitig-MPHF indexing (global offset vs. ID+rank), and the new obipipeline library architecture with parallel workers, biased scheduling, and error handling.

This commit is contained in:

Eric Coissac

2026-05-01 09:33:26 +02:00

parent 4e26e3bd40

commit 27f5e88a7b

72 changed files with 10093 additions and 1626 deletions

									
										src/obikseq/Cargo.toml
									
		+2
		
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				@@ -5,6 +5,8 @@ edition = "2024"

				[dependencies]

				bitvec = "1"

				serde = { version = "1.0", features = ["derive"] }

				serde_json = "1.0.149"

				xxhash-rust = { version = "0.8.15", features = ["xxh3", "const_xxh3"] }

				[dev-dependencies]